Advances in biophysical methods for protein detection and characterisation

Proteins are the building blocs of life and mediate nearly every function in the cell. They are therefore a major and incredibly wide research topic. Their functions and malfunctions have serious impacts on a wide range of diseases. Proteins may be used as extremely versatile tools for biology such as for gene editing or biological medical products. Developing novel methods for protein detection and characterisation may thus have a tremendous impact on modern medicine and research. The present thesis discusses advances in biophysical methods for protein detection and characterisation. First, the possibility of detecting proteins label-free is addressed. A label may change the behaviour of the target protein. Two approaches are investigated: An ultraviolet light based autofluorescence microscope is described; and scattering based detection is explored by expending on the existing interferometric scattering (iSCAT) technique. An oblique illumination approach helps with increasing the contrast of the data, and a time correlation technique is used for local sizing on chip. Second, microfluidic techniques are routinely used to create protein assays. These assays minimise the amount of sample required and the absence of turbulences enable new techniques. A method to easily add nanofluidics elements to microfluidic designs is discussed. Finally, three characterisation methods are described. First, diffusional sizing uses a microfluidic chip to create a concentration gradient. The protein diffusion coefficient is extracted from the time evolution of this gradient. Second, the diffusiophoretic coefficient of the protein can be extracted by diffusiophoresis, which is the motion of proteins driven by the concentration gradient of another solute. This could be an important protein motion mechanism, as many gradients are present in cells and in living beings. Finally, the spatial propagation of the protein amyloid-beta 1-42, a protein associated to neurodegenerative disorders, is observed in a capillary

Visual Servoing from Deep Neural Networks

We present a deep neural network-based method to perform high-precision, robust and real-time 6 DOF visual servoing. The paper describes how to create a dataset simulating various perturbations (occlusions and lighting conditions) from a single real-world image of the scene. A convolutional neural network is fine-tuned using this dataset to estimate the relative pose between two images of the same scene. The output of the network is then employed in a visual servoing control scheme. The method converges robustly even in difficult real-world settings with strong lighting variations and occlusions.A positioning error of less than one millimeter is obtained in experiments with a 6 DOF robot.Comment: fixed authors lis

High performance photonic reservoir computer based on a coherently driven passive cavity

Reservoir computing is a recent bio-inspired approach for processing time-dependent signals. It has enabled a breakthrough in analog information processing, with several experiments, both electronic and optical, demonstrating state-of-the-art performances for hard tasks such as speech recognition, time series prediction and nonlinear channel equalization. A proof-of-principle experiment using a linear optical circuit on a photonic chip to process digital signals was recently reported. Here we present a photonic implementation of a reservoir computer based on a coherently driven passive fiber cavity processing analog signals. Our experiment has error rate as low or lower than previous experiments on a wide variety of tasks, and also has lower power consumption. Furthermore, the analytical model describing our experiment is also of interest, as it constitutes a very simple high performance reservoir computer algorithm. The present experiment, given its good performances, low energy consumption and conceptual simplicity, confirms the great potential of photonic reservoir computing for information processing applications ranging from artificial intelligence to telecommunicationsComment: non

Occurrence cubes : a new paradigm for aggregating species occurrence data

In this paper we describe a method of aggregating species occurrence data into what we coined “occurrence cubes”. The aggregated data can be perceived as a cube with three dimensions - taxonomic, temporal and geographic - and takes into account the spatial uncertainty of each occurrence. The aggregation level of each of the three dimensions can be adapted to the scope. Built on Open Science principles, the method is easily automated and reproducible, and can be used for species trend indicators, maps and distribution models. We are using the method to aggregate species occurrence data for Europe per taxon, year and 1km2 European reference grid, to feed indicators and risk mapping/modelling for the Tracking Invasive Alien Species (TrIAS) project

Laser controlled tunneling in a vertical optical lattice

Raman laser pulses are used to induce coherent tunnelling between neighbouring sites of a vertical 1D optical lattice. Such tunneling occurs when the detuning of a probe laser from the atomic transition frequency matches multiples of the Bloch frequency, allowing for a spectroscopic control of the coupling between Wannier Stark (WS) states. In particular, we prepare coherent superpositions of WS states of adjacent sites, and investigate the coherence time of these superpositions by realizing a spatial interferometer. This scheme provides a powerful tool for coherent manipulation of external degrees of freedom of cold atoms, which is a key issue for quantum information processing

The roles of Eu during the growth of eutectic Si in Al-Si alloys

Controlling the growth of eutectic Si and thereby modifying the eutectic Si from flake-like to fibrous is a key factor in improving the properties of Al-Si alloys. To date, it is generally accepted that the impurity-induced twinning (IIT) mechanism and the twin plane re-entrant edge (TPRE) mechanism as well as poisoning of the TPRE mechanism are valid under certain conditions. However, IIT, TPRE or poisoning of the TPRE mechanism cannot be used to interpret all observations. Here, we report an atomic-scale experimental and theoretical investigation on the roles of Eu during the growth of eutectic Si in Al-Si alloys. Both experimental and theoretical investigations reveal three different roles: (i) the adsorption at the intersection of Si facets, inducing IIT mechanism, (ii) the adsorption at the twin plane re-entrant edge, inducing TPRE mechanism or poisoning of the TPRE mechanism, and (iii) the segregation ahead of the growing Si twins, inducing a solute entrainment within eutectic Si. This investigation not only demonstrates a direct experimental support to the well-accepted poisoning of the TPRE and IIT mechanisms, but also provides a full picture about the roles of Eu atoms during the growth of eutectic Si, including the solute entrainment within eutectic Si

Predictive factors of success at the French National Ranking Examination (NRE) : a retrospective study of the student performance from a French medical school

Background The national ranking examination (NRE) marks the end of the second cycle (6th university year) of French medical studies and ranks students allowing them to choose their specialty and city of residency. We studied the potential predictive factors of success at the 2015 NRE by students attending a French School of Medicine. Methods From March 2016 to March 2017, a retrospective study of factors associated with the 2015 NRE success was conducted and enrolled 242 students who attended their sixth year at the school of medicine of Reims. Demographic and academic data collected by a home-made survey was studied using univariate and then multivariate analysis by generalized linear regression with a threshold of p <  0.05 deemed significant. Results The factors independently associated with a better ranking at the NRE were the motivation for the preparation of the NRE (gain of 3327 ± 527 places, p <  0.0001); to have participated in the NRE white test organized by la Revue du Praticien in November 2014 (gain of 869 ± 426 places, p <  0.04), to have participated in the NRE white test organized by la conférence Hippocrate in March 2015 (+ 613 places ±297, p <  0.04). The factors independently associated with poor NRE ranking were repeating the first year (loss of 1410 places ±286, p <  0.0001), repeating a year during university course (loss of 1092 places ±385, p <  0.005), attendance of hospital internships in 6th year (loss of 706 places ±298, p <  0.02). Conclusions The student motivation and their white tests completion were significantly associated with success at the NRE. Conversely, repeating a university year during their course and attendance of 6th year hospital internships were associated with a lower ranking

Taste-Changing in Staggered Quarks

We present results from a systematic perturbative investigation of taste-changing in improved staggered quarks. We show one-loop taste-changing interactions can be removed perturbatively by an effective four-quark term and calculate the necessary coefficients.Comment: 3 pages using espcrc2.sty and amsmath.sty, 1 Feynman diagram using feynmp.sty for Lattice2002(improve

Testing Lorentz symmetry with planetary orbital dynamics

Planetary ephemerides are a very powerful tool to constrain deviations from the theory of General Relativity using orbital dynamics. The effective field theory framework called the Standard-Model Extension (SME) has been developed in order to systematically parametrize hypothetical violations of Lorentz symmetry (in the Standard Model and in the gravitational sector). In this communication, we use the latest determinations of the supplementary advances of the perihelia and of the nodes obtained by planetary ephemerides analysis to constrain SME coefficients from the pure gravity sector and also from gravity-matter couplings. Our results do not show any deviation from GR and they improve current constraints. Moreover, combinations with existing constraints from Lunar Laser Ranging and from atom interferometry gravimetry allow us to disentangle contributions from the pure gravity sector from the gravity-matter couplings.Comment: 12 pages, 2 figures, version accepted for publication in Phys. Rev.